first commit

defaults

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+{   
+    "gatk_docker":"registry.cn-shanghai.aliyuncs.com/shaolab2023_docker/gatk4:4.5.0.0_1",
+    "gatk4_database":"oss://database-shaolab/gatk4_database/"
+    "gatk_cluster":"OnDemand bcs.es.r.2xlarge img-ubuntu-vpc",
+    "disk_size":"300"
+}

inputs

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+{
+  "{{ project_name }}.gatk_docker": "{{ gatk_docker }}",
+  "{{ project_name }}.sample_id": "{{ sample_id }}",
+  "{{ project_name }}.normal_bam": "{{ normal_bam }}",
+  "{{ project_name }}.normal_bai": "{{ normal_bai }}",
+  "{{ project_name }}.gatk4_database": "{{ gatk4_database }}",
+  "{{ project_name }}.gatk_cluster": "{{ gatk_cluster }}",
+  "{{ project_name }}.disk_size": "{{ disk_size }}"
+}

tasks/gatk.wdl

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+task gatk {
+    String sample_id
+    File normal_bam
+    File normal_bai
+    File gatk4_database
+
+    String docker
+    String cluster
+    String disk_size
+
+    command <<<
+
+        set -o pipefail
+        set -e
+        cp -r ${gatk4_database} ./gatk4_database
+        cp ${normal_bam} ./${sample_id}.bam
+        cp ${normal_bai} ./${sample_id}.bam.bai
+        hg38_genome="./gatk4_database/GRCh38.d1.vd1.fa"
+        dbsnp="./gatk4_database/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz"
+        indel1="./gatk4_database/resources_broad_hg38_v0_Homo_sapiens_assembly38.known_indels.vcf.gz"
+        indel2="./gatk4_database/resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
+        bed="./gatk4_database/test.bed"
+        pon="./gatk4_database/somatic-hg38_1000g_pon.hg38.vcf.gz"
+        EXAC="./gatk4_database/somatic-hg38_small_exac_common_3.hg38.vcf.gz"
+        
+        mkdir markduplicate
+        mkdir BQSR
+        mkdir Mutect2
+        mkdir gatk4_resource
+
+        java -jar -Xmx40g /opt/picard.jar MarkDuplicates INPUT=./${sample_id}.bam OUTPUT=./markduplicate/${sample_id}_marked.bam METRICS_FILE=./markduplicate/${sample_id}.metrics
+        echo "dedup done"
+
+        samtools index -@ 6 ./markduplicate/${sample_id}_marked.bam
+        gatk --java-options "-Djava.io.tmpdir=./BQSR -Xms40G -Xmx40G -XX:ParallelGCThreads=2" BaseRecalibrator -I ./markduplicate/${sample_id}_marked.bam  -R $hg38_genome  -O ./BQSR/${sample_id}_markdup_bqsr.report   --known-sites $dbsnp   --known-sites $indel1   --known-sites $indel2 -L $bed
+
+        gatk --java-options "-Djava.io.tmpdir=./BQSR -Xms40G -Xmx40G -XX:ParallelGCThreads=2" ApplyBQSR  -I ./markduplicate/${sample_id}_marked.bam  -R $hg38_genome -L $bed --bqsr-recal-file ./BQSR/${sample_id}_markdup_bqsr.report   -O ./BQSR/${sample_id}_markdup_bqsr.bam
+        echo "BQSR done"
+
+        gatk --java-options "-Djava.io.tmpdir=./BQSR -Xms40G -Xmx40G -XX:ParallelGCThreads=2" Mutect2 -R $hg38_genome -I ./BQSR/${sample_id}_markdup_bqsr.bam  -L $bed --pon $pon --germline-resource $dbsnp --tumor-lod-to-emit 2 --f1r2-tar-gz Mutect2/${sample_id}.f1r2.tar.gz  -O Mutect2/${sample_id}_mutect2_raw.vcf
+        echo "Mutect2 done"
+
+        gatk --java-options "-Djava.io.tmpdir=./BQSR -Xms40G -Xmx40G -XX:ParallelGCThreads=2" GetPileupSummaries -R $hg38_genome -I ./BQSR/${sample_id}_markdup_bqsr.bam  -V $EXAC -L $EXAC -L $bed --interval-set-rule INTERSECTION  -O Mutect2/${sample_id}.getpileupsum.table
+
+        gatk --java-options "-Djava.io.tmpdir=./BQSR -Xms40G -Xmx40G -XX:ParallelGCThreads=2" CalculateContamination -I Mutect2/${sample_id}.getpileupsum.table  -O Mutect2/${sample_id}.contamination.table --tumor-segmentation Mutect2/${sample_id}.segmentation.table
+
+        gatk --java-options "-Djava.io.tmpdir=./BQSR -Xms40G -Xmx40G -XX:ParallelGCThreads=2" LearnReadOrientationModel -I Mutect2/${sample_id}.f1r2.tar.gz  -O Mutect2/${sample_id}_f1r2_artifact.tar.gz
+
+        gatk --java-options "-Djava.io.tmpdir=./BQSR -Xms40G -Xmx40G -XX:ParallelGCThreads=2" FilterMutectCalls  -V Mutect2/${sample_id}_mutect2_raw.vcf  -R $hg38_genome  --contamination-table Mutect2/${sample_id}.contamination.table --tumor-segmentation Mutect2/${sample_id}.segmentation.table  --ob-priors Mutect2/${sample_id}_f1r2_artifact.tar.gz  -O Mutect2/${sample_id}_mutect2_filtered.vcf
+        bcftools norm -f $hg38_genome -O v  -o Mutect2/${sample_id}_mutect2_filtered_bcfed.vcf  Mutect2/${sample_id}_mutect2_filtered.vcf
+
+
+    >>>
+
+    runtime {
+        docker : docker
+        cluster: cluster
+        systemDisk: "cloud_ssd 100"
+        dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
+    }
+
+    output {
+        File raw_vcf = "./Mutect2/${sample_id}_mutect2_raw.vcf"
+        File filtered_vcf = "./Mutect2/${sample_id}_mutect2_filtered.vcf"
+    }
+
+}
+
+

workflow.wdl

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+import "./tasks/gatk.wdl" as gatk
+workflow {{ project_name }} {
+    String sample_id
+    File normal_bam
+    File normal_bai
+    File gatk4_database
+
+    String gatk_docker
+    String gatk_cluster
+    String disk_size
+
+        call gatk.gatk as gatk {
+                input:	
+                sample_id=sample_id,
+                normal_bam=normal_bam,
+                normal_bai=normal_bai,
+                gatk4_database=gatk4_database,
+                docker=gatk_docker,
+                cluster=gatk_cluster,
+                disk_size=disk_size
+        }
+
+
+}